RNA-Seq: a revolutionary tool for transcriptomics
TLDR
The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.Abstract:
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.read more
Citations
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Journal ArticleDOI
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li,Colin N. Dewey +1 more
TL;DR: It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Journal ArticleDOI
A scaling normalization method for differential expression analysis of RNA-seq data
TL;DR: A simple and effective method for performing normalization is outlined and dramatically improved results for inferring differential expression in simulated and publicly available data sets are shown.
Journal ArticleDOI
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
TL;DR: GEPIA (Gene Expression Profiling Interactive Analysis) fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources.
References
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Journal ArticleDOI
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,Zhong Wang,Karl Waern,C. Shou,Debasish Raha,Mark Gerstein,Michael Snyder +6 more
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
Journal ArticleDOI
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Ryan Lister,Ronan C. O'Malley,Julian Tonti-Filippini,Brian D. Gregory,Charles C. Berry,A. Harvey Millar,Joseph R. Ecker +6 more
TL;DR: Deep sequencing of smRNAs revealed a direct relationship between the location of sm RNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylisation, and a tendency for smRN as to direct strand-specific DNA methylations in regions of RNA-DNA homology.
Journal Article
Serial analysis of gene expression
TL;DR: Serial analysis of gene expression (SAGE) is a sequenced-based technique, which permits comprehensive and quantitative gene expression profiles from specific tissues or cells, which has been successfully applied for transcriptome research and identification of differentially expressed genes between mRNA populations.
Journal ArticleDOI
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays
Sydney Brenner,Maria Johnson,John Bridgham,George Stefan Golda,David H. Lloyd,Davida Johnson,Shujun Luo,Sarah N. McCurdy,Michael F. Foy,Mark Ewan,Rithy Roth,Dave George,Sam Eletr,Glenn Albrecht,Eric Vermaas,Steven Williams,Keith Moon,Timothy Burcham,Michael C. Pallas,Robert B. Dubridge,James W. Kirchner,Karen L. Fearon,Jen-I Mao,Kevin Corcoran +23 more
TL;DR: A novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 μm diameter microbeads provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes.
Journal ArticleDOI
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
Marc Sultan,Marcel H. Schulz,Marcel H. Schulz,Hugues Richard,Alon Magen,Andreas Klingenhoff,Matthias Scherf,Martin Seifert,Tatjana Borodina,Aleksey V. Soldatov,Dmitri Parkhomchuk,Dominic Schmidt,Sean O'Keeffe,Stefan A. Haas,Martin Vingron,Hans Lehrach,Marie-Laure Yaspo +16 more
TL;DR: A global survey of messenger RNA splicing events identified 94,241 splice junctions and showed that exon skipping is the most prevalent form of alternative splicing.
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